You can use Edit | Remove Sequence to delete sequences from a multiple sequence alignment.
This command is enabled when an MSA window is selected and the alignment is unlocked. If necessary, click on the padlock button to display an open padlock.
1. Select the name of a sequence you want to delete. To select more than one sequence, hold down the Shift key and click on the required names.
2. Choose Edit | Delete Sequence to delete the sequences.
For more information, see Editing alignments.